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This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see CompGO.

An R pipeline for .bed file annotation, statistical comparison of GO term enrichment between gene sets and data visualisation

Bioconductor version: 3.3

This package contains functions to accomplish several tasks. It is able to download full genome databases from UCSC, import .bed files easily, annotate these .bed file regions with genes (plus distance) from aforementioned database dumps, interface with DAVID to create functional annotation and gene ontology enrichment charts based on gene lists (such as those generated from input .bed files), statistically compare gene ontology enrichment between multiple experiments and finally visualise and compare these enrichments using directed acyclic graphs or scatterplots. CompGO also enables clustering of experiments based on their GO profiles and provides functions for performing and visualising principle component analysis.

Author: Sam D. Bassett [aut], Ashley J. Waardenberg [aut, cre]

Maintainer: Ashley J. Waardenberg <awaardenberg at>

Citation (from within R, enter citation("CompGO")):


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PDF CompGO-vignette.pdf
PDF R Script Introduction
PDF   Reference Manual
Text   NEWS


biocViews GO, GeneSetEnrichment, MultipleComparison, Software, Visualization
Version 1.8.1
In Bioconductor since BioC 2.14 (R-3.1) (2.5 years)
License GPL-2
Depends RDAVIDWebService
Imports rtracklayer, Rgraphviz, ggplot2, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, pcaMethods, reshape2, pathview
Depends On Me
Imports Me
Suggests Me
Build Report  

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